5-88367793-C-T

Variant names:

• chr5-88367793-C-T
• rs10514299
• ENST00000501715.6:n.578-42280C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000501715.6(TMEM161B-DT):​n.578-42280C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,854 control chromosomes in the GnomAD database, including 3,563 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3563 hom., cov: 32)
• Consequence: TMEM161B-DT ENST00000501715.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 22 publications found

Genes affected

TMEM161B-DT (HGNC:43839): (TMEM161B divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM161B-DT	NR_039993.1	n.207-42280C>T		intron_variant	Intron 2 of 3
TMEM161B-DT	NR_039994.2	n.165-42280C>T		intron_variant	Intron 2 of 3
TMEM161B-DT	NR_039995.1	n.207-68480C>T		intron_variant	Intron 2 of 2
TMEM161B-DT	NR_105019.1	n.586-42280C>T		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM161B-DT	ENST00000501715.6	n.578-42280C>T		intron_variant	Intron 6 of 7	1
TMEM161B-DT	ENST00000501869.7	n.198-42280C>T		intron_variant	Intron 2 of 4	1
TMEM161B-DT	ENST00000504922.8	n.246-68480C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32275 AN: 151736 Hom.: 3562 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.199

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.213 AC: 32298 AN: 151854 Hom.: 3563 Cov.: 32 AF XY: 0.209 AC XY: 15522 AN XY: 74194

African (AFR) AF: 0.180 AC: 7447 AN: 41452

American (AMR) AF: 0.154 AC: 2338 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3460

East Asian (EAS) AF: 0.192 AC: 991 AN: 5152

South Asian (SAS) AF: 0.144 AC: 695 AN: 4820

European-Finnish (FIN) AF: 0.259 AC: 2736 AN: 10568

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16591 AN: 67870

Other (OTH) AF: 0.199 AC: 420 AN: 2110

Alfa AF: 0.232 Hom.: 17475

Bravo AF: 0.204

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.80
PhyloP100		-0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10514299; hg19: chr5-87663610;